Methods and compositions for increasing susceptibility to radiation treatment by inhibiting suppression of numerical chromosomal instability of cancer cells

ABSTRACT

Disclosed is a method for increasing susceptibility of cancer cells to ionizing radiation by delivering to the cells a radiosensitizing agent that has one of the following properties: (a) it perturbs the process of chromosome segregation thereby increasing chromosome missegregation; or (b) it is an inhibitor of an agent that promotes faithful chromosome segregation induces numeric chromosome instability in said cells and this instability is induced substantially simultaneously with or closely prior to or closely after irradiating the cells. Examples of such radiosensitizing agent include inhibitors of one or more of the following: Kif2b, MCAK, MPS1, Eg5/Kinesin-5 5, Polo-like kinase 4, MCAK, Bub1 and Hec1. Such agents specifically target proteins involved in maintaining or promoting faithful chromosome segregation.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.16/818,966, filed Mar. 13, 2020, which is a continuation of U.S. patentapplication Ser. No. 15/544,811, filed Jul. 19, 2017, which is aNational Stage Application of PCT/US2016/014400, filed Jan. 21, 2016,which claims priority to U.S. Provisional Patent Application No.62/106,204, filed Jan. 21, 2015, the entire contents of each of which isincorporated herein by reference.

GOVERNMENT SUPPORT

This invention was made with government support under GM051542 awardedby the National Institutes of Health. The government has certain rightsin the invention.

BACKGROUND OF THE DISCLOSURE Technical Field

The present disclosure relates to the field of cancer therapy usingagents that promote whole-chromosomal instability, as irradiationsensitization agents, and thus to make patients more sensitive toradiation therapy, thereby increasing the effect of radiation therapy.

Background and Description of Related Art Radiation therapy is anintegral modality in cancer treatment. The lethal effect of ionizingradiation (IR) lies in its ability to cause widespread genomic damageprimarily in the form of DNA double-strand breaks (DSBs). Each Gray (Gy)of IR has been proposed to directly induce ˜35 DNA DSBs per cell. Thisoverwhelming damage generally overcomes the ability of tumor cells torepair DSBs, leading to a reduction in cellular viability and to celldeath. DNA damage produced by IR can be repaired through homologousrecombination (HR) and non-homologous end joining (NHEJ). HR repair isless error-prone than NHEJ, as the latter can join DSB ends of genomicDNA, which can lead to chromosomal translocations, acentric chromatinfragments as well as dicentric chromosomes which have two centromeres.Acentric chromatin fragments exhibit a high likelihood of missegregationduring the subsequent mitosis, as they are incapable of establishingcanonical attachment to spindle microtubules at the kinetochores.Alternatively, dicentric chromatin often leads to the formation ofchromatin bridges where each centromere is attached to microtubulesemanating from opposite spindle poles. Forces exerted by the mitoticspindle break chromatin bridges in a process termed thebreakage-fusion-bridge cycle. This cycle can also be initiated bytelomere dysfunction and replication stress. It is thus clear that DNAbreaks generated by IR in dividing cells can directly lead to structuralchromosomal instability (s-CIN), whose hallmarks are chromatin bridgesand acentric chromatin fragments.

Another form of genome instability, present in the majority of solidtumors, is numerical (or whole) chromosomal instability (w-CIN). w-CINprimarily arises from errors in whole chromosome segregation duringmitosis and it generates widespread aneuploidy in tumor cells. Aphenotypic hallmark of w-CIN, both in cell culture and human tumorsamples, is the presence of chromosomes that lag in the middle of themitotic spindle during anaphase. These lagging chromosomes can directlylead to chromosome missegregation and aneuploidy. w-CIN does not existseparately from s-CIN, as it was recently shown that lagging chromosomescan also undergo severe structural damage by generating whole-chromosomecontaining micronuclei. These micronuclei are defective in DNAreplication and repair and possess a faulty nuclear envelope leading tothe pulverization of their enclosed chromosomes. Thus w-CIN can in turnlead to s-CIN.

Given the interrelatedness of w-CIN and s-CIN we asked whether IR coulddirectly generate numerical chromosomal abnormalities. Experimental andclinical evidence suggest that, in addition to direct DNA breaks, IR canlead to changes in chromosome numbers. Furthermore, we recentlydemonstrated that activation of the DNA damage response pathway duringmitosis, using IR or Doxorubicin, directly leads to the formation oflagging chromosomes during anaphase. This suggests that IR has thepotential to generate both w-CIN and s-CIN in a context-dependentmanner.

The sensitivity of cells to IR is not only dependent on the amount ofDNA damage that immediately results from IR exposure; pre-existingdamage or the inability to repair this damage are also importantdeterminants of cellular viability. In the clinical setting, therelationship between s-CIN and IR has long been recognized, wherebygenetically unstable tumors with intrinsically elevated rates of s-CINor decreased DNA repair ability are more likely to respond to radiationtreatment. Accordingly, many known chemotherapeutic agents thatsensitize tumors to ionizing radiation act by either promoting DNAdamage or impairing DNA repair. (It should be noted, however, that thesechemotherapeutic agents are not targeted specifically to increasingwhole chromosome instability.) On the other hand, the role of w-CIN inmediating sensitivity to IR is much less understood. This isparticularly relevant given that mitosis has long been recognized as themost radiosensitive phase of the cell cycle, thus offering a potentiallyimportant therapeutic target. Along these lines, the present inventorsand coworkers recently found that, in patients diagnosed with rectaladenocarcinoma, elevated pre-treatment rates of chromosome segregationerrors forebode superior response to chemoradiation therapy. Thisinspired the present inventors to investigate whether pre-existingdefects related to w-CIN that manifest as lagging chromosomes may alsoplay a role in determining sensitivity to IR. Furthermore, the inventorsasked whether w-CIN can be used to increase or decrease the sensitivityof a dividing cell to ionizing radiation.

SUMMARY OF THE DISCLOSURE

As described herein, the present disclosure provides new experimentalevidence elucidating one of the mechanisms—previously unreported—bywhich cell-cycle dependent vulnerability of cancer cells undergoingmitosis to ionizing radiation occurs.

The inventors have shown that treatment with ionizing radiation leads tomitotic chromosome segregation errors in vivo and to long-lastinganeuploidy in tumor-derived cell lines. These mitotic errors generate anabundance of micronuclei that predispose chromosomes to subsequentcatastrophic pulverization by IR thereby independently amplifyingradiation-induced genome damage. Experimentally suppressing wholechromosome missegregation (which if not supported would lead tonumerical or whole chromosome instability) reduces downstreamchromosomal defects and significantly increases the viability ofirradiated mitotic cells, giving rise to tumor cell resistance tofurther radiation. Further, orthotopically transplanted humanglioblastoma tumors in which chromosome missegregation rates have beenreduced through overexpression of kinesins are rendered markedly moreresistant to ionizing radiation, exhibiting diminished markers of celldeath in response to radiation treatment. This disclosure thusidentifies a novel mitotic pathway for radiation-induced genome damage,which occurs outside the primary nucleus and augments chromosomalbreaks. This relationship between radiation treatment and wholechromosome missegregation can be exploited to enhance efficacy ofradiation treatments of solid malignant tumors susceptible to radiationtreatment and thus to reduce the likelihood of resistance. It can alsobe used to spare noncancerous tissues or organs from deleterious effectsof radiation.

Accordingly, in one aspect, the present disclosure provides a method forincreasing susceptibility of cancer cells to ionizing radiation to aradiosensitizing agent that has one of the following properties: (a) itperturbs the process of chromosome segregation thereby increasingchromosome missegregation; or (b) it is an inhibitor of an agent thatpromotes faithful chromosome segregation induces numeric chromosomeinstability in said cells and this instability is induced substantiallysimultaneously with or closely prior to or closely after irradiating thecells.

In some embodiments the radiosensitizing agent inhibits one or more ofthe following directly or indirectly: Kif2b, MCAK, MPS1, Eg5/Kinesin-5,Polo-like kinase 4, MCAK, Bub1 and Hec1. The agent thus specificallytargets proteins involved in maintaining or promoting faithfulchromosome segregation.

In some embodiments, the cancer cells are solid tumor cancer cells forwhich radiation is an indicated therapeutic modality. Nonlimitingexamples of such tumors include head-and-neck cancer, rectaladenocarcinoma, glioblastoma multiform.

In some embodiments, the radiosensitizing agent is selected from thegroup consisting of MPS1 inhibitors, Eg5/Kinesin-5 inhibitors, Polo-likekinase 4 inhibitors, MCAK inhibitors, Bub1 inhibitors and Hec1inhibitors. (Bub1 and Hec1 inhibitors will produce the desiredchromosomal instability but so will activators as described below.)

The ionizing radiation is administered in one or in multiple (at leasttwo) divided doses.

In another aspect, the present disclosure provides a method forincreasing cytotoxicity of ionizing radiation in a subject to be treatedfor a solid malignant tumor susceptible to treatment with ionizingradiation, the method comprising administering systemically to thesubject or locally to the tumor an inhibitor of suppression of numericalchromosome instability incident to a first dose of said radiation,thereby enhancing chromosome missegregation during mitosis substantiallysimultaneously with or closely preceding treatment of the tumor with asubsequent dose of ionizing radiation. This subsequent dose can bedelivered either closely before, closely after or up to 1 or even 2months after increasing chromosomal instability as long as thechromosomal instability induction substantially persists.

A method is also provided for reducing damage of noncancerous cells ortissue incident to ionizing radiation aimed at cancerous cells or tissuecomprising exposing the noncancerous cells or tissue to aradioprotective agent (such as agonists of Kif2b or MCAK) which is anenhancer of suppression of chromosome missegregation and reduces numericchromosome instability in said cells simultaneously with or immediatelyprior to or immediately following irradiating the cancerous cells ortissue with a therapeutically effective dose and regimen of ionizingradiation.

The radioprotective agent is or specifically activates a proteininvolved in faithful chromosome segregation maintenance.

In some embodiments, the radioprotective agent is Kif2b or MCAK or anagonist or activator of Kif2b or MCAK.

A clarifying detail is that presence of initial chromosome instabilityin a cell makes the cell more susceptible to induction of furtherchromosome instability by the methods recited above; conversely,presence of initial chromosome stability in a cell makes a cell morelikely to respond to a radioprotective agent. Thus, in accordance withthe present methods, w-CIN in induced preferentially in cancer cells.Main contributors to cancer cell specificity are the following: 1)induction of w-CIN according to the present disclosure occurs mostly inrapidly dividing cells (such as cancer cells); and 2) the higherchromosomal missegregation before treatment, the more sensitive cellsare to interventions aimed at further increasing w-CIN.

In some embodiments, the tumor includes, but is not limited to tumors ofthe following organs: the skin, breast, brain, cervix, testis, heart,lung, gastrointestinal tract, genitourinary tract, liver, bone, nervoussystem, reproductive system, and adrenal glands. In more detail, adrenaltumors include for example adrenocortical carcinoma, bile duct, bladder,bone (e.g., Ewing's sarcoma, osteosarcoma, malignant fibroushistiocytoma), brain/CNS (e.g., astrocytoma, glioma, glioblastoma,childhood tumors, such as atypical teratoid/rhabdoid tumor, germ celltumor, embryonal tumor, ependymoma), breast (including withoutlimitation ductal carcinoma in situ, carcinoma, cervical, colon/rectum,endometrial, esophageal, eye (e.g., melanoma, retinoblastoma),gallbladder, gastrointestinal, kidney (e.g., renal cell, Wilms' tumor),heart, head and neck, laryngeal and hypopharyngeal, liver, lung, oral(e.g., lip, mouth, salivary gland) mesothelioma, nasopharyngeal,neuroblastoma, ovarian, pancreatic, peritoneal, pituitary, prostate,retinoblastoma, rhabdomyosarcoma, salivary gland, sarcoma (e.g.,Kaposi's sarcoma), skin (e.g., squamous cell carcinoma, basal cellcarcinoma, melanoma), small intestine, stomach, soft tissue sarcoma(such as fibrosarcoma), rhabdomyosarcoma, testicular, thymus, thyroid,parathyroid, uterine (including without limitation endometrial,fallopian tube), and vaginal tumor and the metastasis thereof. In someembodiments, the tumor is selected from the group consisting of breast,lung, GI tract, skin, and soft tissue tumors. In some furtherembodiments the tumor is selected from the group consisting of breast,lung, GI tract and prostate tumors.

The present inventors thus have discovered that increasing chromosomemissegregation together with radiation treatment would lead tosensitization of the tumor to radiation therapy. This in turn permits 1)to decrease dose of radiation and achieve the same effect, 2) tomaintain dose of radiation and increase tumor sensitization in otherwiseresistant tumors, 3) to increase radioprotection of normal organs.

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A-1E are a combination of high-resolution immunofluorescencemicroscopy images and graphical representation thereof showing thatw-CIN is induced by IR in vitro. FIG. 1A are examples of U251 cellsfixed 25 min after exposure to 12 Gy and exhibiting lagging chromosomes(LC), chromatin bridges (CB), acentric chromatin (AC) or a combination(LC+AC) obtained through high-resolution fluorescence microscopy. Scalebar, m. FIG. 1B is a series of bar graphs showing percentage ofchromosome missegregation in anaphase spindles of RPE1, HCT116 and U251cells as a function of IR dose. Bars represents mean±s.e.m., n=150cells, three experiments, *P<0.01, two-tailed t-test. FIG. 1C are imagesobtained by FISH showing HCT116 nuclei stained for DNA (grey cloud rightpanel), centromere (white dots right panel) and telomere (white dots onthe outer edges of grey cloud right panel) probes for human chromosome2. White arrow denotes an aneuploid nucleus containing three copies ofchromosome 2. Scale bar, 10 m. FIG. 1D is a bar graph showing percentHCT116 nuclei containing whole-chromosome and segmental aneuploidy forchromosome 2. n=300 cells, *P<0.05. FIG. 1E is a bar graph showingpercentage of chromosome missegregation in anaphase spindles of HCT116p53^(−/−) cells exposed to 0 Gy (top) or 6 Gy (bottom) as a function oftime after irradiation (mo, months) FIGS. 2A-2E show in vivo inductionof chromosome segregation errors by IR.

FIGS. 2A and 2D are schematic representations of experimental design.FIG. 2B is an image of H&E staining of SC-HCT116 p53^(−/−) xenografts.FIG. 2C is a graph showing percentage of anaphase cells exhibitinglagging chromosome in response to IR. FIG. 2E is a graph oftumor-derived cells karyotype analysis.

FIGS. 3A-3C show that IR-induced chromosome segregation errors lead towidespread chromosomal damage. FIGS. 3A and 3D are schematicrepresentations of experimental design. FIG. 3B is an image of cellscontaining micronucleus. FIG. 3C is a graph depicting percentage ofcells containing micronuclei as a function of IR dose. FIG. 3E is animage of mitotic spread containing pulverized chromosomes. FIG. 3F is agraph showing percentage of mitotic spreads. FIG. 3G is an image ofcells containing micronuclei. FIG. 3H is a graph of γ-H2AX fluorescenceintensity following IR. FIG. 3I is a graph showing a percentage ofanaphase spindles containing lagging chromosomes as a function of IRdose.

FIGS. 4A-4C show that Kif2b overexpression does not alter IR-induced DNAbreaks or repair. FIG. 4A is a graph showing fluorescence intensity ofγ-H2AX in Kif2b overexpression cells. FIG. 4B is a graph showing theaverage number of γ-H2AX foci per nucleus as a function of IR dose inKif2b overexpression cells. FIG. 4C is a series of images of cellsstained for DNA and γ-H2AX following IR.

FIGS. 5A-5B show that chromosome segregation errors alter the viabilityof irradiated mitotic cells. FIGS. 5A and 5B are graphs of survivingfraction of cells versus radiation dose.

FIGS. 6A-6L show that reducing chromosome segregation errors inducesradiation resistance in vivo. FIG. 6A is a schematic representation ofexperimental design. FIG. 6B are bioluminescence images of mice. FIG. 6Cis a graph showing normalized bioluminescence over time in xenografts.FIG. 6D is an image showing H&E staining. FIG. 6E is an image showingKi67 positive cells. FIG. 6F is a graph showing percentage of Ki67positive cells. FIG. 6G is a graph showing mitotic count in U251xenografts. FIG. 6H is an image of atypical mitotic cells. FIG. 6I is agraph showing a percent of atypical mitotic cells in xenografts. FIG. 6Jis an image showing cleaved caspase 3 (CC3) tumor. FIG. 6K is a graphshowing quantification of CC3 positive cells. FIG. 6L is a schematicrepresentation linking IR to chromosome segregation errors anddownstream chromosomal structural defects.

FIGS. 7A-7C illustrate chromosome segregation errors in irradiatedmitotic cells. FIGS. 7A and 7B are images of anaphase spindle in U251cells. FIG. 7C is an autoradiograph of a Western blot of U251 cellsstained with GFP and DM1-α antibodies.

FIGS. 8A-8C show that overexpression of Kif2b alters viability ofirradiated mitotic cells without altering basal growth rates or ploidyin culture. FIG. 8A is a plot of surviving cellular fraction andradiation dose. FIG. 8B is a plot of number of cells per plate as afunction of time. FIG. 8C is a bar graph showing karyotypic distributionof GFP-expressing and GFP-Kif2b expressing U251 cells.

FIG. 9 is a plot of absolute bioluminescence signal as a function oftime after intracranial injection of U251 cells expressing GFP orGFP-Kif2b. Data derived from a sample experiment. IR treatment (24 Gytotal) was administered starting on day 18 with 4 Gy fractions everyother day. The experiment was performed with three animals in each armand was replicated three times. The data shows that Kif2b overexpressionleads to tumor radiation resistance. Error bars show the standard errorof the mean (SEM) of animals within an arm of a representativeexperiment.

FIG. 10 is an autoradiograph of a Western blot showing Kinesin-13overexpression in U251 cells. Upper autoradiograph is a Western blot ofU251 cells expressing GFP-tagged kinesin-13 proteins Kif2b (lane 1),Kif2b (lane 2), MCAK (lane 3), and GFP (lane 4) stained using anti-GFPantibodies. DM1-α antibody was used to blot for α-tubulin as a loadingcontrol (lower autoradiograph). Molecular weight markers (in kDa) aredepicted on the left side of the immunoblots.

FIGS. 11A-11C show computational models of w-CIN in clonally expandingpopulations. FIG. 11A is a schematic of cancer cells, which frequentlymissegregate whole chromosomes leading to karyotypic heterogeneity.FIGS. 11B and 11C are distribution curves showing respectively thedependence of clonal fitness (FIG. 11B) and adaptive capacity (FIG. 11C)on chromosome missegregation rates (pmisseg) for diploid andtetraploid-derived clonal populations.

DETAILED DESCRIPTION

The present disclosure is based on the following discoveries:

Definitions

As used herein, the following terms and abbreviations shall have themeaning ascribed to them below unless the context clearly indicatesotherwise.

“Subject” means a patient (human or veterinary) or an experimentalanimal, such as a mouse or other rodent.

“Time interval of increased susceptibility” means the period of timeafter administration of the CIN promoting agent, or radiosensitizingagent during which the resulting increase in w-CIN or laggingchromosomes is still substantially present.

“Effective amount” is an amount of a radiosensitizing agent or aradioprotective agent according to the present disclosure sufficient toincrease or to decrease w-CIn by at least 5%. This amount varies greatlyfrom agent to agent and may also vary widely (from picograms tomilligrams perkilogram of patient weight) according to the tumor and theage and physical condition of the patient as well as other factors.Examples and guidance of effective amounts are provided in thediscussion of particular agents.

The term “ionizing radiation” means any radiation where a nuclearparticle has sufficient energy to remove an electron or proton or otherparticle from an atom or molecule, thus producing an ion and a freeelectron or radical. Examples of such ionizing radiation include, butare not limited to, gamma rays, X-rays, protons, electrons, alphaparticles, carbon atoms, or particles emitted from a radioactive sourceincluding, but not limited to, yttrium and radium. Radiation fromimplanted material is included. Ionizing radiation is commonly used inmedical radiotherapy and the specific techniques for such treatment willbe apparent to a person of ordinary skill in the art. Other examples ofradiation suitable for use in the present methods are provided elsewherein the specification.

The term “radiosensitizing agent” means agents which increase thesusceptibility of cells to the damaging effects of ionizing radiation orwhich become more toxic to a cell after exposure of the cell to ionizingradiation. A radiosensitizing agent may permit lower doses of radiationto be administered and still provide a therapeutically effective dose.In the context of the present disclosure, agents that increasechromosome missegregation by specifically targeting proteins that areinvolved in chromosome missegregation (activating such proteins) or infaithful chromosome segregation (inhibiting such proteins) areradiosensitizing agents.

Conversely, those agents that suppress (or more accurately increase thesuppression of) chromosome missegregation can be referred to as“radioprotective agents.” The latter have the property of enhancingsuppression of chromosomal missegregation and reducing numericchromosomal instability.

“Closely” in the context of timing of administration means during aninterval of increased radiosensitization of a cancerous cell (while theinduced w-CIN substantially persists). This interval can be as short asabout 1 hour to about 8 hours, but may extend to about 24 hours, or upto about 1 month or even 2 prior to an irradiation dose depending on theduration of induced w-CIN.

“Substantially” in the context of a measurable property means “mostly,”or “a major portion of” (for example 50% or more). Thus a cellsubstantially retaining induced w-CIN means retaining at least abouthalf of the induced increase in w-CIN perpetrated by a radiosensitizingagent. CIN is considered increased by reference to an untreated cell idit is at least 5% higher than the chromosomal instability of anuntreated cell. “Substantially” in the context of “substantiallysimultaneously” mean at the same time or almost at the same time, e.g.,within the same day or 24-hour period.

“Tumor” as used herein means primary or metastatic tumor and includesthe list of the tumor in the summary, above.

Radiation Therapy

The present disclosure provides for sensitization of tumours toradiation therapy, where radiation therapy can include any radiationused in cancer treatment. The radiation may be curative, adjuvant, orpalliative radiotherapy. Such radiation includes, but is not limited to,various forms of ionizing radiation (e.g, as listed supra), externalbeam radiotherapy (EBRT or XBRT) or teletherapy, brachytherapy or sealedsource therapy, radioactive implant therapy, intraoperativeradiotherapy, and unsealed source radiotherapy.

In some embodiments, the radiation is ionizing radiation. Radiation maybe electromagnetic or particulate in nature. Electromagnetic radiationincludes, but is not limited to, x-rays and gamma rays. Particulateradiation includes, but is not limited to, electron beams, proton beans,neutron beams, alpha particles, and negative pimesons. The unit ofabsorbed dose is the gray (Gy), which is defined as the absorption of 1joule per kilogram. As is appreciated by those of skill in the art, theenergy of the radiation determines the depth of absorption as well asthe nature of the atomic interaction. Radiotherapy can be administeredby a conventional radiological treatment apparatus and methods, or byintraoperative and stereotactic methods. Radiation may also be deliveredby other methods that include, but are not limited to, targeteddelivery, systemic delivery of targeted radioactive conjugates andintracavitary techniques (brachytherapy). Other radiation methods notdescribed above can also be used to practice this invention.

In accordance with the present disclosure, ionizing radiation is used totarget tissues or cells, such as neoplastic tissues or cells, forselective delivery of an CIN promoting active agent via a deliveryvehicle comprising the active agent. Thus, the target tissues or cellsare exposed to ionizing radiation, and a delivery vehicle comprising theactive CIN promoting agent is administered before, during, or bothbefore and during the exposure to radiation. Radiation immediatelypreceding delivery of the CIN promoting agent to the tumor is alsopossible or even 2.

In one embodiment, radiation therapy is delivered using radioactiveisotopes (brachytherapy). This can be either high-dose rate or low doserate brachytherapy. High dose rate brachytherapy is usually deliveredusing Ir-192 (but not exclusively) and can be given in one or more dosesand doses. Low dose rate brachytherapy can be delivered usingradioactive palladium or iodine and it involves permanent or long-termplacement of seeds in and around the target and dose delivery obeys thehalf-life of the decay of the radioactive substance and can take weeksto months to deliver the majority of the dose.

In particular embodiments, the methods described herein can be used inthe treatment of various types of solid tumors. Examples of solid tumorshave been provided in the Summary of the Disclosure.

In more detail, malignant tumors which can be treated by methodsdescribed herein can be used in the treatment of cancer, include withoutlimitation adrenal tumors (e.g., adrenocortical carcinoma), anal, bileduct, bladder, bone tumors (e.g., Ewing's sarcoma, osteosarcoma,malignant fibrous histiocytoma), brain/CNS (tumors e.g., astrocytoma,glioma, glioblastoma, childhood tumors, such as atypicalteratoid/rhabdoid tumor, germ cell tumor, embryonal tumor, ependymoma),breast tumors (including without limitation ductal carcinoma in situ,carcinoma, cervical, colon/rectum, endometrial, esophageal, eye (e.g.,melanoma, retinoblastoma), gallbladder, gastrointestinal, kidney (e.g.,renal cell, Wilms' tumor), heart, head and neck, laryngeal andhypopharyngeal, liver, lung, oral (e.g., lip, mouth, salivary gland)mesothelioma, nasopharyngeal, neuroblastoma, ovarian, pancreatic,peritoneal, pituitary, prostate, retinoblastoma, rhabdomyosarcoma,salivary gland, sarcoma (e.g., Kaposi's sarcoma), skin (e.g., squamouscell carcinoma, basal cell carcinoma, melanoma), small intestine,stomach, soft tissue sarcoma (such as fibrosarcoma), rhabdomyosarcoma,testicular, thymus, thyroid, parathyroid, uterine (including withoutlimitation endometrial, fallopian tube), and vaginal tumor and themetastases thereof. In some embodiments, the tumor is selected from thegroup consisting of breast, lung, GI tract, skin, and soft tissuetumors.

Radiation Dosage and Administration Regimen

Administration of radiation can be made by any appropriate means knownto those of ordinary skill in the art. Radiation can be suitablyadministered in a dose effective for the particular cancer to betreated, as determined by a person of ordinary skill in the art. Thedose of radiation used in conjunction with the agents that specificallypromote w-CIN may be similar to the amount administered when radiationis used alone, or, may be reduced. In some instances, the dosage ofradiation may be determined in relation to tumor volume and may dependon the type of tumor being treated. The dosage may also take intoaccount other factors that can be determined by an ordinarily skilledclinician.

Radiation treatment may be given as fractionated doses or as a bolusdose. For example, radiation can be administered in a range of 1 toabout 50 fractions, with each fraction size being within the range of0.1 to about 50 Gy. In some embodiments, dosage of each fraction isabout 2 to about 30 Gy. In other embodiments, dosage of each fraction isabout 4 to about 25 Gy. In yet other embodiments, dosage of eachfraction is about 10 to about 20 Gy. Particular dosage amounts include,but are not limited to, 0.4 (or 40 cGY), 1, 2, 4, 10 and 20 Gy.

In some embodiments, the source of ionizing radiation comprises anexternal beam photon irradiation source, which is typically utilized atenergy levels ranging from about 10 kV (KeV) to about 18 MV (MeV) perphoton beam, or a brachytherapy source directly applied in the tumorcavity. These sources of radiation can include, but are not limited to,yttrium, radium. In some embodiments, the source of ionizing radiationcomprises an external beam electron irradiation source, which istypically utilized at energy levels ranging from about 10 KeV to about20 MeV per electron beam. In some embodiments, the source of ionizingradiation comprises an external beam proton irradiation source, which istypically utilized at energy levels ranging from about 10 MEV to about300 MeV per proton beam.

In the case of external beam radiation therapy, appropriate blocks,wedges, and boluses are used to deliver adequate dose to the plannedtarget volume of target tissue. A preferred minimum source-axis distancecomprises about 80 cm but can range considerably up and down as thoseskilled in the art appreciate. The subject receives local-regionalirradiation via fields that are designed to encompass sites of diseaserequiring palliation or primary treatment while endeavoring to sparenoncancerous tissue as much as possible.

Study, site, treatment intent and normal tissue considerations are alsoevaluated in the determination of dose. Examples of preferred dosagesranges are as follows. For an ionizing radiation dose that isadministered in 1 fraction, a preferred dosage range comprises about 500to about 1500 cGy, and at times 2400 cGy, with a preferred dosage rangecomprising about 800 to about 1200 cGy. For an ionizing radiation dosethat is administered in 5 fractions, a preferred dosage range comprisesabout 1000 to about 3000 cGy, and at times up to 800 cGy, with apreferred dosage range comprising about 1500 to about 2500 cGy, and witha more preferred dosage amount comprising about 200 cGy. For an ionizingradiation dose that is administered in 10 fractions, a preferred dosagerange comprises about 1000 to about 6000 cGy, with a preferred dosagerange comprising about 2000 to about 4000 cGy, and with a more preferreddosage amount comprising about 3000 cGy.

For an ionizing radiation dose that is administered in 15 fractions, apreferred dosage range comprises about 1000 to about 7000 cGy, with apreferred dosage range comprising about 2000 to about 5000 cGy, and witha more preferred dosage amount comprising about 3500 CGy. For anionizing radiation dose that is administered in 30 fractions, apreferred dosage range comprises about 2000 to about 12000 cGy, with apreferred dosage range comprising about 4000 to about 8000 cGy, and witha more preferred dosage amount comprising about 6000 cGy.

In some embodiments, radiation is administered 1 to about 50 times.Frequency of radiation treatment can be from 3 times per day to aboutonce per month. In further embodiments, radiation is administered onceper 3 weeks, once per 2 weeks, once per week, 2-6 times per week, atleast once a day, twice a day or three times a day, or any combinationthereof. For example, a suitable administration regimen includes aschedule where fractionations are given 2 times per day for 2 daysfollowed by a month long pause, and this cycle is repeated numeroustimes.

Treatment can be administered for 2-8 consecutive or non-consecutiveweeks. Whether given as a bolus or as fractionated doses, total dose ofradiation may be, for example, about 2-200 Gy in 2 Gy fractions or anequivalent biological dose using other fractionation schemes. These arejust examples of radiation treatment protocols, and the presentdisclosure encompasses other treatment protocols that may be determinedby a clinician of ordinary skill in the art.

Actual dosage levels of the agent that promotes CIN and radiation may bevaried so as to obtain the desired therapeutic response for a particularsubject, composition and mode of administration, without being toxic tothe subject. The selected dosage level will depend upon a variety offactors, including the route of administration, the rate of breakdown ofthe active form of the CIN promoting agent, the duration of treatment,other drugs, compounds, and/or materials used in combination with theparticular CIN promoting agent, the age, sex, weight, condition, generalhealth and prior medical history of the patient being treated, andsimilar relevant factors well known in the art.

When used as disclosed in the present disclosure, ionizing radiation maybe used in the same amount and administration regimen. However, it maybe possible through the use of radiosensitizing (and converselyradioprotective) agents to lower the dose or the frequency ofadministration, or both. Conversely, it may be possible to increase thesame if used in combination with radioprotective agents. As statedabove, methods for fine tuning the radiation intensity and frequency ofadministration are known in the art.

In one embodiment, high dose rate brachytherapy is given in one or moredoses, where doses can range anywhere from about 0.1 Gy to about 50 Gy.In another embodiment, high dose rate brachytherapy is administeredintra-operatively. In yet another embodiment, low dose ratebrachytherapy is delivered using radioactive palladium or iodine and itinvolves permanent or long-term placement of seeds in and around thetarget and dose delivery obeys the half-life of the decay of theradioactive substance and can take weeks to months to deliver themajority of the dose. Furthermore, it is estimated that dose isdelivered at a rate of anywhere between 0.001 Gy-1 Gy/hour in low-doserate brachytherapy

The therapeutic combination of the present disclosure can be combinedwith other cancer therapies, including, but not limited to, adjuncttherapies (such as, but not limited to, surgical tumor resection andchemotherapy). Resection is often a standard procedure for the treatmentof tumours. The types of surgery that may be used in combination withthe present invention include, but are not limited to, preventative,curative and palliative surgery, and any other method that would becontemplated by those of skill in the art.

Agents that Promote/Induce Numeric Chromosome Instability

The agents in the categories described below all alter chromosomemissegragation and eventually cause w-CIN by either specificallyinhibiting Kif2b, MCAK, MPS1, Eg5/Kinesin-5, Polo-like kinase 4, Mad2,Hec1, Bub1, or BubR1 or by activating Mad2, Hec1, BubR1, or Bub1.

Inhibition of Kif2b and MCAK as Means of Inducing w-CIN

The present disclosure provides evidence that over-expression of themicrotubule-depolymerizing kinesin-13 proteins, Kif2b or MCAK, whichlocalize to the attachment sites of chromosomes to spindle microtubulesat the kinetochores, leads to the suppression of w-CIN in otherwisechromosomally unstable cell This suppression is persistent, lasting morethan 30 days both in vitro and in vivo studies. Furthermore, Kif2boverexpressing cells displayed greater than twofold reduction inchromosome segregation errors during anaphase, which led to radiationresistance in vivo (FIG. 3I). These findings indicate that theinhibition of proteins that localize to the attachment sites ofchromosomes to spindle microtubules at the kinetochores can be used toincrease w-CIN in cancer cells and as such promote radiosensitization.

In one embodiment, suitable agents that induce numeric chromosomalinstability are those that inhibit proteins that localize to theattachment sites of chromosomes to spindle microtubules at thekinetochores during mitosis. Proteins known to localize to theattachment sites of chromosomes to spindle microtubules at thekinetochores during mitosis include, but are not limited to Kif2b andMCAK. Thus, in one embodiment, suitable agents that induce numericchromosomal instability are those that specifically target and inhibitKif2b or MCAK.

Kif2b belongs to the kinesin-13 family of proteins and localizes tokinetochores during early mitosis (Manning A L et al. Mol. Biol. Cell.18:2970-2979 (2007)). For example, Kif2b can be inhibited using agentsthat inhibit Kif2b specifically. One such agent is DHTP((Z)-2-(4-((5-(4-chlorophenyl)-6-(isopropoxycarbonyl)-7-methyl-3-oxo-3,5-dihydro-2H-thiazolo[3,2-a]pyrimidin-2-ylidene)methyl)phenoxy)aceticacid). DHTP has been shown to be a potent compound that inhibitskinein-13 induced microtubule depolymerization, where the IC₅₀ of DHTPin inhibiting Kif2b is 1.2 μM (FEBS Lett. 27; 588(14):2315-20 (2014)).In addition to Kif2b, DHTP possesses inhibitory activity against MCAK,with the IC₅₀ of DHTP in inhibiting MCAK is 4.6 μM FEBS Lett. 27;588(14):2315-20 (2014)).

Additionally, Kif2b can be inhibited using agents that inhibit Kif2bspecifically but indirectly (e.g., through specific activation orinhibition of another protein that inhibits or activates Kif2b). Thepossibility of such indirect specific effect is not limited to Kif2b butin principle extends to any radiosensitizing or radioprotective agentemployed in the present methods.

Additional examples of MCAK inhibitors include MCAKsv1. See US PatentApplication US20060177828 (Alternatively spliced isoform of mitoticcentromere-associated kinesin (MCAK), Armour, Christopher, et al.;Filing Date Sep. 16, 2004; Publication Date Aug. 10, 2006).

Inhibition of MPS1 as Means of Inducing CIN

The core SAC kinases monopolar spindle-1 (Mps1, also known as TTK) is aserine threonine kinase which functions as a core component of thespindle assembly checkpoint (SAC) (Lauze' et al. EMBO J. 14, 1655-1663,(1995)), a key surveillance mechanism that monitors the attachment ofspindle microtubules to the kinetochores of the chromosomes duringpro-metaphase and halts the transitions to anaphase until allchromosomes are bi-oriented, fully attached, and correctly tensed at themetaphase plate. Mps1 is expressed in the mitosis phase of the cellcycle in proliferating cells. Mps1 activity causes cells to prematurelyexit mitosis with unattached chromosomes, resulting in severe chromosomemissegregation and aneuploidy (Colombo et al. Cancer Res., 70,10255-10264 (2010); Jemaa et al. Cell Death Differ. 20, 1532-1545(2013)). Overexpression of Mps1 has been observed in several cancer celllines and tumor types including lung and breast cancers, where higherMps1 levels correlate with worse prognosis.

Established anti-mitotic drugs such as vinca alkaloids, taxanes, orepothilones activate SAC either by destabilizing or stabilizing spindlemicrotubules resulting in mitotic arrest. Prolonged arrest in mitosisforces a cell either into a mitotic exit without cytokinesis or into amitotic catastrophe leading to cell death. Such drugs do not targetchromosome missegregation or faithful segregation specifically and arenot included within the specifically acting agents of the presentdisclosure. In contrast to anti-mitotic drugs, specific Mps1 inhibitorsinactivate the SAC and accelerate progression of cells through mitosiseventually resulting in severe chromosomal missegregation, mitoticcatastrophe, and cell death. Consequently, Mps1 inhibition leads tofailure of cells to arrest in mitosis in response to anti-mitotic drugs.Thus, the combination of microtubule-interfering agents and Mps1inhibition strongly increases chromosomal segregation errors and celldeath and therefore, constitutes an efficient strategy for selectivelyeliminating tumor cells.

Known Mps1 inhibitors include, but are not limited to BAY 1161909(Bayer, Mps1 IC₅₀=1.9 nM, currently in Phase I (ClinicalTrials.gov ID:NCT02138812_(An Open-label Phase I Dose-escalation Study to Characterizethe Safety, Tolerability, Pharmacokinetics, and Maximum Tolerated Doseof Oral BAY1161909 in Combination With Weekly Intravenous PaclitaxelGiven in an Intermittent Dosing Schedule in Subjects With AdvancedMalignancies), Mason et al. Cancer Cell, 26, 163-176, (2014)), BAY1217389 (Bayer, Mps1 IC₅₀=1.1 nM, currently in Phase I(ClinicalTrials.gov ID: NCT02366949 (Phase I Study of Oral BAY 1217389in Combination With Intravenous Paclitaxel)), S81694 (Nerviano MedicalSciences, Mps1 IC₅₀=3 nM, currently in pre-clinical development,(Colombo et al. Cancer Res., 70, 10255-10264 (2010)), and CFI-402257(University Health Network,tdc.uhnresearch.ca/opportunities/small-molecule-tyrosine-threonine-ttkmps1-inhibitor/).BAY 1161909 has been administered orally, with a starting dose of 0.75mg twice daily, on a 14-day cycle—D1, D2, D8, D9 and 28 day cycle—D8, D9D15 and D16 of a 28 day cycle.

Other non-limiting examples of specific Mps1 inhibitors includeN-(4-{2-[(2-cyanophenyl)amino][1,2,4]triazolo[1,5-a]pyridin-6-yl}phenyl)-2-phenylacetamide(Mps-BAY1) (a triazolopyridine),N-cyclopropyl-4-{8-[(2-methylpropyl)amino]-6-(quinolin-5-yl)imidazo[1,2-a]pyrazin-3-yl}benzamide(Mps-BAY2a), andN-cyclopropyl-4-{8-(isobutylamino)imidazo[1,2-a]pyrazin-3-yl}benzamide(Mps-BAY2b).

In their recent publication (published after the priority date of thepresent disclosure), Maachani et al. (Mol Cancer Res. 13(5):852-62(2015)) used NMS-P715 Mps inhibitor (100 mg/kg) and showed thatinhibition of Mps1 enhances radiosensitization of human glioblastoma.While the authors did not explore increase in CIN as a potentialmechanism for the observed radiosensitivity, their results corroboratecertain findings of the present disclosure, in particular thatinhibition of protein/or molecules that promote faithful chromosomesegregation leads to increased susceptibility of cancer cells toradiation therapy. Furthermore, the results observed by Maachani et al.suggest that Mps1 is required for cell survival following irradiation ofGBM cells but is not required for the survival of normal cells.

Inhibition of Eg5/Kinesin as Means of Inducing CIN

Eg5, a member of the kinesin superfamily, plays a key role in mitosis,as it is required for the formation of a bipolar spindle. Eg5 controlsmitosis through bipolar spindle formation and thus chromosome separation(Blangy et al. Cell, 83, 1159-1169 (1995)). Eg5 is overexpressed in manyproliferative tissues including leukemia as well as solid tumors such asbreast, lung, ovarian, bladder and pancreatic cancers (Hedge et al.Proc. Am. Soc. Clin. Oncol., 22 (2003), Ding et al. Int. J. Urol., 18,432-438 (2011), Liu et al. J. Pathol., 221, 221-228 (2010)). Given therole that Eg5 plays in promoting faithful chromosomal segregation, thefindings of the present disclosure indicate that specifically targetingand inhibiting Eg5 in cancer cells leads to radiosensitization of suchcells.

Known Eg5 inhibitors include, but are not limited to 4SC-205, currentlyin Phase I Clinical Trial (ClinicalTrials.gov ID: NCT01065025, OpenLabel, Dose Escalation Trial of Oral Eg5 Kinesin-spindle Inhibitor4SC-205 in Patients With Advanced Malignancies (AEGIS); and AZD4877,which was part of a Phase I trial in patients with solid and lymphoidmalignancies (Gerecitano et al. Invest New Drugs. (2):355-62 (2013)).4SC-205 was administered once or twice weekly at doses of 25 mg-200 mg.In case of AZD4877, a standard 3+3 dose-escalation design was used,where AZD4877 was given as an intravenous infusion on days 1, 4, 8 and11 of each 21-day cycle (Gerecitano et al. Invest New Drugs. (2):355-62(2013)).

Additional nonlimiting examples of specific Eg5 inhibitors includemonastrol (IC₅₀=30 μM), enastron, dimethylenastron, S-trityl-l-cysteine(STLC), ispinesib, and HR22C16 where some of these inhibitors arecurrently in phase I or II clinical trials as anticancer drugs(El-Nassan H B, Eur J Med Chem. 62:614-31 (2013). For further detailsregarding Eg5 inhibitors please refer to El-Nassan H B, Eur J Med Chem.62:614-31 (2013).

Additionally, specific Eg5 inhibitors have been shown to be effectiveagainst taxol-resistant cancer cells (Marcus et al. J. Biol. Chem., 280(2005)). Therefore, given the findings of the present disclosure,combining inhibition of proteins that promote faithful segregation ofchromosomes with radiation therapy can offer new treatment solutions fortumors resistant to other therapies.

Inhibition of Polo-Like Kinase 4 (PLK4) as Means of Inducing CIN

PLK4 is a conserved key regulator of centriole duplication(Bettencourt-Dias et al. Curr. Biol. 15, 2199-2207 (2005)).Dysregulation of PLK4 expression causes loss of centrosome numeralintegrity, which promotes genomic instability (Ganem et al. Nature 460,278-282 (2009). Thus, in some embodiment, the present disclosurecomprises the use of PLK4 inhibitors in cancer cells in order togenerate cancer cells more susceptible to radiation therapy compared tocancer cells that not treated with PLK4 inhibitor prior to radiationtherapy.

Small molecules that specifically target and inhibit the kinase activityof PLK4 have been identified (Mason et al., Cancer Cell 26, 163-176(2014); Wong et al. Science 348, 1155-1160, (2015)), and one of theseinhibitors, CFI-400945 is currently in phase I clinical testing(ClinicalTrials.gov Identifier: NCT01954316). CFI-400945 exhibits a PLK4IC₅₀=2.8 nM, and PLK K_(i)=0.26 nM. Ongoing clinical trial studyinvolves testing of the CFI-400945 fumarate tablets, with dose levels of3, 6, 11, 16, 24, and 32 mg/day. In mice, CFI-400945 has been used atdosages of 2.5-20 mg/kg (Mason et al., Cancer Cell 26, 163-176 (2014)).

Wong et al. (Science 348, 1155-1160, (2015)) have recently reported 2highly selective PLK4 inhibitors, centrinone [LCR-263; inhibitionconstant (Ki)=0.16 nM in vitro; centrosome depletion at 100 nM] andcentrinone-B (LCR-323; Ki=0.6 nM in vitro; centrosome depletion at 500nM).

Additionally, the PLK4 inhibitor R1530 downregulates the expression ofmitotic checkpoint kinase BubR1, which in leads to polyploidy (Tovar etal. Cell Cycle. 9(16):3364-75 (2010)).

A more detailed discussion regarding the inhibition of PLK4 in cancertreatment is described by Holland and Cleveland. Cancer Cell.26(2):151-3 (2014)).

Inhibition or Activation of Bub Kinases as Means of Inducing CIN

BubR1 and Bub1 are paralogous serine/threonine kinases that performdifferent functions in the spindle assembly checkpoint (SAC). BubR1associates with unattached kinetochores, contributes to stabilizingkinetochore-MT attachments and aligning chromosomes, and forms part ofthe mitotic checkpoint complex (MCC). During mitosis, Bub1 bindskinetochores and plays a key role in establishing the mitotic spindlecheckpoint and aligning chromosomes in addition to its central role inensuring fidelity during chromosomal segregation into daughter cells (Yuet al. 4:262-265 (2005)). Bub1 transgenic mice develop aneuploid tumors(Ricke, et al. J. Cell Biol. 193, 1049-1064 (2011)).

Recently, Brazeau and Rosse (ACS Med Chem Lett. 5(4): 280-281 (2014))reported a development of series of cycloalkenepyrazoles, which are ableto target and specifically inhibit Bub1 kinase. Additionally, 2OH-BNPP1is a potent inhibitor of Bub1 with IC₅₀s around 250 nM (Kang et al. MolCell. 32(3): 394-405. (2008), Nyati et al. Sci Signal. 6; 8(358)(2015)). Such agents are suitable for use in the present methods.

Down-regulation of BubR1 by oncogenic protein breast cancer-specificgene 1 (BCSG1)-mediated inhibition has been observed in advanced stagebreast cancer and is believe to promote chromosomal instability (CIN).Thus, according to the present disclosure, one example of strategysuitable for radiosensitization is the inhibition of Bub1 and BubR1.

Paradoxically, reports have also suggested that BubR1 overexpressionleads to high incidence of aneuploidy coupled with malignant progression(Ando et al. Cancer Sci. 101:639-645 (2010)). Based on the abovestudies, it appears that BubR1 at basal level functions to preventmissegregation of sister chromatids during mitosis, but either gain orloss of BubR1 expression promote CIN-driven tumorigenesis and cancerprogression. Thus, the inventors anticipate that either inhibition ofactivation of BubR1, as well as Bub1 can be manipulated in order toachieve proper radiosensitization. For activation of BubR1, a smallmolecule agonist could be developed through a chemical screen.

Inhibition or Activation of Mad2 and Hec1 as Means of Inducing CIN

As mammalian cells proceed from prometaphase to metaphase, a signallingcomplex that contains mitotic arrest deficient 1 (MAD1), MAD2, Mps1,BuB1, BuB3 and BuBR1 assembles at unoccupied kinetochores. Mad2 is acentral component of the spindle assembly checkpoint, which is afeedback control that prevents cells with incompletely assembledspindles from leaving mitosis. Partial loss of checkpoint control, viadeletion of one MAD2 allele results in a defective mitotic checkpoint inhuman cancer cells, leading to an increased rate of chromosomemissegregation events and an increased frequency of aneuploid metaphasescompared to cells control cancer cells (Michel et al. Nature 409,355-359 (2001)). Thus, based on the consequences (induction of CIN) ofMAD2 loss in cancer cells, as well as on the findings of the presentdisclosure, use of specific Mad2 inhibitors in conjunction withradiation therapy is anticipated to lead to enhanced tumor treatmentresponse.

Recently, Kastl et al. identified a specific MAD2 inhibitor-1 (M2I-1),the first small molecule inhibitor targeting the binding of Mad2 toCdc20, an essential protein-protein interaction (PPI) within the SAC(Kastl et al. ACS Chem. Biol., 10 (7) 1661-1666 (2015)).

Hec1 (Highly Expressed in Cancer 1) is one of four proteins of the outerkinetochore Ndc80 complex involved in the dynamic interface betweencentromeres and spindle microtubules. Inhibition of Hec1 phosphorylationabrogates microtubule attachment to the kinetochore and induceschromosome missegregation, underscoring the importance of Hec1phosphorylation in faithful chromosome segregation and the maintenanceof genomic stability in mitosis (Du et al. Oncogene. 27(29):4107-14(2008)). Thus, inhibition of Hec1 is another method by which w-CIN canbe induced, leading to radiosensitization of cancer cells and tumors.

Examples of Hec1 inhibitors include, but are not limited to TAI-95 andTAI-1 (Huang et al. Mol Cancer Ther. 13(6):1419-30 (2014), Huang et al.J Exp Clin Cancer_Res. 33:6, (2014)). TAI-95 is highly potent in breastcancer cell lines, with GI₅₀ between 14.29 and 73.65 nmol/L.Furthermore, TAI-95 showed excellent oral efficacy in an in vivo breastcancer model, where mice were treated with TAI-95 twice a day for 28days, using TAI-95 orally at 10, 25, 50 mg/kg (mpk) or intravenously at10, 25, 50 mpk (Huang et al. Mol Cancer Ther. 13(6):1419-30 (2014). Incase of TAI-1, TAI-1 was shown to be effective orally in in vivo animalmodels of triple negative breast cancer, colon cancer and liver cancer.Furthermore, a 7-day toxicology studies of TAI-1 in mice showed nosignificant change in body weight, organ weight, and plasma indices whenanimals were treated with 7.5, 22.5, and 75.0 mg/kg twice a day by oraladministration (Huang et al. J Exp Clin Cancer Res. 33:6, (2014).

It is important to emphasize that for certain mitotic checkpoint genesknown to be implicated in tumors, such as Mad2 and Hec1, both partialinactivation and overactivation of the mitotic checkpoint promotechromosomal instability. For example, Hec1 overexpression hyperactivatesthe mitotic checkpoint and induces tumor formation in vivo(Diaz-Rodriguez et al. Proc Natl Acad Sci USA. 105(43):16719-24 (2008)).Furthermore, overexpression of Hec1 resulted in lagging chromosomes andaneuploidy (Diaz-Rodriguez et al. Proc Natl Acad Sci USA.105(43):16719-24 (2008)). Thus, in addition to the inhibition of Hec1 asa means of radiosensitization, activation or upregulation of Hec1 canalso be used to promote CIN, resulting in radiosensitization. Inaddition to development of agents that can promote activation or causeupregulation of Hec1, this can also be achieved by altering thephosphorylation patterns of Hec1, which can make Hec1 more stable,causing it to latch onto microtubules more strongly, and leading toincreased stability and increased chromosome missegregation.

In addition to Hec1, Mad2 overexpression has also been shown to promoteaneuploidy and tumorigenesis in mice (Sotillo et al. Cancer Cell.11:9-23 (2007)). Thus, agents that cause activation of upregulation ofMad2 (and lead to checkpoint hyperactivity) can also be used to promoteradiosensitization.

Noncoding RNA Activated by DNA Damage (NORAD)

Long noncoding RNAs (lncRNAs) have emerged as regulators of diversebiological processes. Recently, Lee at al. performed a functionalanalysis of a poorly characterized human lncRNA (LINC00657) that isinduced after DNA damage, which they termed “noncoding RNA activated byDNA damage”, or NORAD (Lee at al. Cell. 164(1-2):69-80 (2016)). Theauthors showed that inactivation of NORAD triggers dramatic aneuploidyin previously karyotypically stable cell lines. They further discoveredthat NORAD maintains genomic stability by sequestering PUMILIO proteins,which repress the stability and translation of mRNAs to which they bind.

Thus, in light of findings disclosed herein, it is anticipated thatinhibition of NORAD can also be used for radiosensitization.

Antibodies Against Target Proteins

In addition to inhibitors discussed above, specific inhibition of Kif2b,MCAK, MPS1, Eg5/Kinesin-5, Polo-like kinase 4, Mad2, and Hec1 can beachieved using monoclonal or polyclonal antibodies and related specificbinding moieties such as immunoreactive fragments thereof.

Table 1 lists nonlimiting examples of commercially availablehuman-specific monoclonal or polyclonal antibodies against each of theseproteins.

Target Commercially Available Antibody Protein (Catalog Number) Kif2bNBP1-89446 (Novus Biologicals, Littleton, CO); CPBT-38621RH (CreativeDiagnostics, Shirley, NY). MCAK ab42676 (Abcam, Cambridge MA); (M01),clone 1G2 (Abnova, Walnut, CA MPS1 [N1] (ab11108) (Abcam, Cambridge,MA); (7E3) (MA5-15523) (Thermo Fisher Scientific, Waltham, MA)Eg5/Kinesin-5 10C7/Eg5 (Bio Legend, San Diego, CA) PA5-28933 (ThermoFisher Scientific, Waltham, MA) PLK4 [36-298] (ab17057) (Abcam,Cambridge, MA); A300-251A (Bethyl Laboratories Montgomery, TX) Mad2ENZ-ABS169-0200 (Enzo Life Sciences, Farmingdale, NY); sc-393188 (SantaCruz Biotechnology, Dallas, Texas) Hec1 ab3613 (Abcam, Cambridge, MA);A300- 771A (Bethyl Laboratories Montgomery, TX)

Threshold Levels of Inhibition or Activation of Target Protein

In previous sections, means by which target proteins can be inhibited oractivated for the purposes of inducing w-CIN and consequentlyradiosensitization were described. In this section, the inventorsprovide approximate threshold levels for inhibition or activation oftarget genes, wherein such threshold levels are expected to providelevels of target genes sufficient for induction of w-CIN4 andradiosensitization. Table 2 includes approximate threshold levels forinhibition of genes that promote faithful chromosome segregation, whileTable 3 provides such threshold levels for activation of genes thatpromote chromosome missegragation.

TABLE 2 Increase in CIN via inhibition of genes that promote faithfulchromosome segregation. Genes that promote faithful chromosomesegregation Threshold Levels of Inhibition Kif2b 1.5-fold or more MCAK 2fold or more MPS1 2 fold or more. Severe inhibition can result incheckpoint and arrest. Eg5/Kinesin-5 5-fold (would need be reversibleinhibition to avoid mitotic arrest in the case of non-reversibleinhibition) PLK4 2 fold or more

TABLE 3 Increase in CIN via activation of genes that promote chromosomemissegragation. Genes that promote chromosome Threshold Levelsmisssegregation of Activation MAD2 2-3 fold BUBR1 2-3 fold HEC1 >3-fold

In addition to methods of inhibition discussed in prior sections, it isnoted that target genes and proteins can be reduced or inhibited at anylevel, including the protein, RNA, or DNA level. Furthermore, anytechniques known in the art that are used for reducing protein, RNA, orDNA levels can be used to achieve increase in w-CIN4 andradiosensitization. Such techniques include, but are not limited to genedeletion, gene disruption, shRNA or antisense approaches. Additionally,gene modification (gene editing) can be achieved using an engineerednuclease such as a zinc finger nuclease (ZFP), TALE-nuclease (TALEN), orCRISPR/Cas nuclease.

Kif2b and MCAK as Radioprotective Agents

Activation or overexpression of proteins that promote faithfulchromosome segregation can be used as a method of protection ofnoncancerous cells against radiation. Since overexpression of Kif2bresults in decreased CIN, agents that activate or upregulate Kif2b canbe used as radioprotectors. Such radioprotectors can serve to protectnoncancerous cells preferentially as the radiation intensity is focusedon the tumor (e.g., in conformal radiation), making any radioprotectorin the tumor cells practically ineffective. Furthermore, radioprotectorscan alternatively be used to shield and protect organs or tissues. Forexample, the digestive tract can be protected by delivering aradio-protector that is not systemically absorbed but it can have atopical or local effect on the tract, which tends to receive the mostdamage of ionizing radiation. Such organs include, but are not limitedto the pharynx, esophagus, stomach, small and large intestines, andrectum. This approach to tissue protection can also be applied to othermucosal surface such as the vaginal tract and the cervix.

Based on the findings of the present disclosure, it is anticipated thatany agent that specifically promotes faithful chromosome segregation,and reduction in lagging chromosomes and/or CIN could be used as aradioprotective agent.

The inventors reserve the right to disclaim any agent disclosed herein,radiosensitizing or radioprotective, that is deemed to deprive theclaimed invention of novelty or inventiveness (render it obvious).Methods for Detection of w-CIN

The CIN status of tumors is not routinely evaluated in the clinicalsetting even though a large amount of data collected from human tumorssuggests that aneuploidy has a causative role in tumorigenesis byshowing that CIN and chromosomal aberrations correlate with tumor grade(Carter et al. Nature Genet. 38, 1043-1048 (2006), Kronenwett, U. et al.Cancer Res. 64, 904-909 (2004)).

Fluorescence in situ hybridization (FISH) is one of the main methods forthe assessment of w-CIN status in tumors. Variations in chromosome copynumber across the cell population can be quantified using fluorescentlylabeled DNA probes that bind to the centromeres of specific chromosomes.FISH thus allows the assessment of the chromosomal state of hundreds ofcells, and the rate of change can be inferred from the cell-to-cellvariability in chromosome number (Speicer et al. Nat Rev Genet 6:782-792 (2005)).

Additional methods for assessing w-CIN status include, but are notlimited to flow and DNA image cytometry. These methods have beendiscussed by Darzynkiewicz et al. Adv Exp Med Biol 676: 137-147 (2010)).Both of these methods measure cellular DNA content through the use ofdyes that bind stoichiometrically to DNA, allowing DNA cell cycledistribution and ploidy to be determined. The ability of cytometrytechniques to identify w-CIN in tumors is supported by the observationthat anaphase bridges are only observed in tumors defined as CIN bycytometry in a small cohort of sarcomas, colorectal and pancreaticcarcinomas (Fiegler et al., Nucleic Acids Res 35: e15 (2007)).

Single-cell, comparative genomic hybridization (CGH) (Fiegler et al.,Nucleic Acids Res 35: e15 (2007)) can yield information on bothnumerical and structural chromosomal aberrations at a single-cell level,and heterogeneity can then be quantified by comparing multiple cells.Karyotypic complexity measures of CIN are commonly performed on acombined population of cells. Conventional array CGH uses DNA frommultiple cells, and can be used to define the both structuralchromosomal complexity and copy number changes in a tumor sample (Pinkelet al. Nat Genet 37: S11-S17 (2005)).

Methods for w-CIN assessment are discussed in detail by McGranahan etal. EMBO Rep. 13(6): 528-538 (2012)). Chromosomal instability can alsobe assessed directly by measuring the frequency of lagging chromosomesin dividing cells undergoing anaphase or telophase. This has been shownin Diffuse Large B Cell Lymphoma as well as rectal cancer but is viablein most tumor specimens where surgical or core biopsies or excisionexist and the tissue is either stained using standard Hematoxylin andEosin staining, immunofluorescence or immunohistochemistry. In thefollowing two papers, the method was used as a prognostic and predictivemarker. See for example” Clin Cancer Res. 2011 Dec. 15; 17(24):7704-11.doi: 10.1158/1078-0432.CCR-11-2049.

Chromosomal instability substantiates poor prognosis in patients withdiffuse large B-cell lymphoma. Bakhoum S F1, Danilova O V, Kaur P, LevyN B, Compton D A. See also, Cancer. 2014 Jun. 1; 120(11):1733-42. doi:10.1002/cncr.28656. Epub 2014 Mar. 6. Chromosomal instability portendssuperior response of rectal adenocarcinoma to chemoradiation therapy.Zaki B I1, Suriawinata A A, Eastman A R, Garner K M, Bakhoum S F

As described above and as illustrated in the Examples below, the presentdisclosure provides novel insights into genome damage induced by IR,beyond direct DNA breaks, which damage occurs outside of the primarynucleus. The inventors have shown that when IR is delivered to mitoticcells, it can directly lead to errors in whole-chromosome segregation,which subsequently leads to the formation of micronuclei and chromosomepulverization hours to days later (FIG. 6I). The type of missegregationerrors in irradiated cells are dependent on the time lapsed after IRexposure. This is likely dependent on the phase of the cell cycle duringwhich cells are irradiated. IR exposure during interphase (G1, S and G2)of the cell cycle would produce DSBs (double strand breaks), which leadto acentric chromatin and chromatin bridges during the subsequentanaphase. This explains the prevalence of chromatin bridges and acentricchromatin 12 h after IR exposure (FIG. 1 ). On the other hand, whencells are irradiated during mitosis this directly leads to the formationof lagging chromosomes. Interestingly, analysis of anaphase spindles 24h, and up to 1 month, after IR exposure reveals chromosomemissegregation patterns suggestive of both w-CIN and s-CIN. This mirrorsrecent work showing that w-CIN and s-CIN coexist in an interdependentmanner (Crasta et al. Nature. 482:53-58, 2012), Bakhoum et al. CancerDiscov. 4:1281-1289 (2014).

The multilayered genomic damage described herein provides an explanationfor the exquisite sensitivity of mitotic cells to IR (Gunderson et al.Clinical Radiation Oncology. Churchill Livingstone; 2011, Terasima etal. Biophys J. 1963; 3:11-33, whereby IR exposure during mitosis notonly leads to direct DNA breaks but also to additional numerical anddownstream structural chromosomal damage. This cell cycle-dependentsensitivity has been exploited in the way radiation treatment isdelivered in clinical settings. A fundamental rationale for dividingradiation treatment dose into small daily fractions is to enact lethaldamage onto the sensitive subpopulation of tumor cells, including themitotic subpopulation, while sparing toxicity to the surrounding normaltissue which typically contains fewer mitotic cells and is more adept atDNA repair (Gunderson et al. Clinical Radiation Oncology. ChurchillLivingstone; 2011. Therefore, fractionated radiation therapy canmaximize damage to mitotic cell population in otherwise non-synchronizedtumors.

The magnitude of the effect of Kif2b overexpression in vivo (Example 8)is surprising given the fact that most of the tumor cell population isnot in M-phase. The inventors postulate that some of this may beaccounted for by the fractionation scheme under which radiation therapywas delivered. Second, when U251 cells were irradiated in vivo theyexhibited an increased rate of atypical mitoses (FIGS. 6H, and 6I).These spindle defects are likely caused by pre-mitotic damage as directIR exposure during mitosis has not been shown to significantly alterspindle geometry (Bakhoum S F, Cancer Discov. 2014; 4:1281-1289). Themechanism of how pre-mitotic irradiation induces spindle damage ispoorly understood. Nonetheless, these atypical spindle geometries havebeen shown to lead to chromosome segregation errors (Ganem N J, Nature.460:278-282 (2009); Silkworth et al. PLoS One. 4:e6564 (2009)). Thus, itis conceivable that the effect of Kif2b overexpression in vivo extendsbeyond the directly irradiated mitotic tumour subpopulation wherebyKif2b suppresses w-CIN indirectly caused by defects in spindle geometryoriginating from pre-mitotic damage. This hypothesis is supported by theobservation that DNA damage-induced cell death is enhanced byprogression through mitosis (Varmark Cell Cycle. 8:2951-2963 (2009)) andthe inventors propose that this is partly due to numerical chromosomalaberration resulting from mitotic chromosome missegregation.

The dependence of irradiated mitotic cell sensitivity on chromosomemissegregation rates offers insight into recent findings where patientsdiagnosed with rectal adenocarcinoma with elevated pre-treatmentchromosome segregation errors were more likely to respond tochemoradiation therapy (Zaki et al. Cancer. 120:1733-1742 (2014)).Interestingly, in this patient cohort, there was a synergisticrelationship in the predictive power between chromosome missegregationand levels of Mre11, a component of the MRN complex involved in therecognition and repair of DSBs (van den Bosch et al. EMBO Rep. 4:844-849(2003). Patients with elevated chromosome missegregation and reducedlevels of Mre11 were significantly more likely to respond tochemoradiation therapy (Zaki et al. Cancer. 120:1733-1742 (2014). Thisindicates that increasing chromosome missegregation rates in mitosis mayincrease the therapeutic potency of IR particularly in the setting ofdecreased repair efficiency of DSBs. Such an approach may already bewithin clinical feasibility as several known chemotherapeutics canincrease chromosome missegregation rates (Thompson et al. J Cell Biol.188:369-381 (2010), Bakhoum et al. J Clin Invest. 122:1138-1143 (2012),Janssen et al. Proc Natl Acad Sci USA. 106:19108-19113 (2009). It canalso be achieved more selectively by developing molecularly targetedinhibitors of the kinesin-13 proteins, Kif2b or MCAK, as discussed indetails in the present disclosure.

The severe structural damage caused by the effect of IR on mitotic cellshas important consequences on the small subset of cells that surviveradiation treatment. Chromosome pulverization has been postulated torepresent a precursor to massive chromosomal rearrangements known aschromothripsis (Stephens et al. Cell. 144:27-40 (2011)). The findings ofthe present disclosure indicate that pulverization is likely deleteriousto cellular viability. In rare instances, however, these punctuatedgenomic alterations could lead to selective advantage and generatehighly aggressive tumors, which represent a rare but devastating lateside-effect of radiation therapy. In conclusion, work described in thepresent disclosure suggests that chromosome pulverization and subsequentchromothripsis would be a defining feature of radiation-inducedsecondary tumors.

EXAMPLES

Materials and Methods:

Cell culture and irradiation. Cells were maintained at 37° C. in a 5%CO₂ atmosphere in Dulbecco's modified medium (DMEM, for U251) or McCoy'smedium (for HCT116) with 10% fetal bovine serum, 50 IU ml-1 penicillin,and 50 mg ml-1 streptomycin. U251 cells were kindly provided from thelaboratory of Mark A. Israel (Geisel School of Medicine at Dartmouth),HCT116 cells (both p53^(+/+) and p53^(−/−) were kindly provided by thelaboratory of Bert Vogelstein (Johns Hopkins University). For plasmidselection, cells were maintained in 0.5-1.0 mg ml-1 of G418 (geneticin).Cells were g-irradiated using a ¹³⁷Cs-irradiator at a rate of 2.38Gy/min or using external beam radiation at 6 MeV delivered by a linearaccelerator according to safety rules of Dartmouth and UCSF.

Antibodies. Tubulin-specific mAb DM1α (Sigma-Aldrich), Anti-centromereantibody (CREST, Dartmouth), Anti-cleaved caspase-3 antibody (CellSignaling), anti-Ki67-antibody (Ventana), anti-g-H2AX-antibody (NovusBiologicals), GFP-specific antibody (William Wickner, Dartmouth).Antibodies were used at dilutions of 1:1000 or 1:10000 (for GFP-specificantibody).

Immunofluorescence imaging. Cells were fixed with 3.5% paraformaldehydeor methanol (−20° C.) for 15 minutes, washed with Tris-buffered salinewith 5% bovine serum albumin (TBS-BSA) and 0.5% Triton X-100 for 5minutes, and TBS-BSA for 5 minutes. Antibodies were diluted inTBS-BSA+0.1% Triton X-100 and coverslips incubated for 3 hours at roomtemperature, then washed with TBS-BSA for 5 minutes. Secondaryantibodies were diluted in TBS-BSA+0.1% Triton X-100 and coverslipsincubated for 1 hour at room temperature. Images were acquired withOrca-ER Hamamatsu cooled CCD camera mounted on an Eclipse TE 2000-ENikon microscope. 0.2 m optical sections in the z-axis were collectedwith a plan Apo 60X 1.4 NA oil immersion objective at room temperature.Iterative restoration was performed using Phylum Live software(Improvision). Quantification of g-H2AX fluorescence levels were doneusing Phylum.

Immunoblots. Membranes were blocked with 0.5% milk in TBS+0.1% Tween for1 hour. Membranes were blotted at room temperature for 3 hours withantibodies at 1:1000. Secondary HRP-conjugated anti-mouse/rabbit(BioRad) were used at 1:2000. Images of uncropped immunoblots aredepicted in FIG. 10 . Western blots of U251 cells expressing GFP-taggedkinesin-13 proteins Kif2b (lane 1), Kif2b (lane 2), MCAK (lane 3), andGFP (lane 4) stained using anti-GFP antibodies. DM1-α antibody was usedto blot for α-tubulin as a loading control. Molecular weight markers (inkDa) are depicted on the left side of the immunoblots (FIG. 10 ).

Fluorescence in situ hybridization. HCT116 p53^(−/−) cells were treatedwith 100 μM monastrol or DMSO control for 8 h and then γ-irradiated.Immediately following irradiation, cells were washed with PBS twice andthen recovered in fresh media for 1 h. For FISH analysis, cells werecollected by trypsinization, briefly resuspended in 75 mM potassiumchloride, fixed, washed twice in 3:1 methanol/acetic acid mix, droppedonto wet slides, air dried, and stained with DAPI. FISH was performedusing both α-satellite and subtelomere probes specific for thecentromeric and q arm telomeric regions of chromosomes 2 respectively(Cytocell). Cells were hybridized according to the manufacturer'sprotocol, and chromosome signals in at least 300 nuclei were scored.

In vivo xenograft HCT116 experiments Animal experiments were approved byInstitutional Animal Cancer and Use Committee at UCSF, in accordancewith institutional and national guidelines. 2-5 million HCT116 p53^(−/−)cells⁴³ were implanted subcutaneously into the flanks of CD1-Nude mice(4-6 week-old males supplied by the UCSF Breeding Core or Jackson Labs).Tumors were measured with calipers. Volume was calculated by thefollowing formula: width²×length×0.5. Tumors were exposed to gammairradiation (¹³⁷Cs) at fractionated doses (5 consecutive days×2 Gy) whentumors were ˜300 mm³ or at a single dose (1 day×10 Gy) when tumors were˜800 mm³. Tumors were isolated and cultured or sectioned forimmunohistochemistry.

Clonogenic assays Cells were either trypsinized (for non-synchronizedpopulations) or collected using mitotic shake-off (for mitoticpopulation) serially diluted and irradiated in their native medium.Cells were then plated in 25-cm² T-flasks and clones were grown for 18days. Clones were stained with Crystal violet and colonies were countedwhen they reached an approximate size of ˜50 cell/clone²⁹. Relativeviability was determined based on the 0 Gy dose.

Automated counting of g-H2AX foci. Cell Profiler 2.0 (Broad Institute)⁴was used to segment nuclei and for automated counting of foci using theexamplesspeckles.cp pipeline. Nuclei were segmented based on their shapeand signal intensity, foci were identified based on their intensity andtheir diameter. Intensity threshold spanned 2.5-100%.

In vivo orthotopic U251 experiments Mouse experiments were approved byand performed according to the guidelines of the Institutional AnimalCancer and Use Committee at UCSF. U251-GFP-Kif2b cells and U251-GFPcells were modified using lentivirus expressing firefly luciferase.Dissociated cells were resuspended in ice-cold DME H-21 medium withoutsupplements at 100,000 cells/ml. 300,000 cells per animal were injectedinto six weeks old athymic mice using the Stoelting stereotacticinjection apparatus and a sharp Hamilton syringe. Mice were anesthetizedwith isofluorane and placed in the stereotactic frame using ear bars andconstant isofluorane supply through a mouthpiece adaptor. A hole wasbored in the skull 1 mm anterior and 0.5 lateral to the Bregma, and 2.5mm below the surface of the brain and cells were injected using manualpressure. Mice were followed by bioluminescence imaging untilluminescence signal indicated that tumors were established. Radiationwas administered at 4 Gy using the JLShepherd @ Associates irradiator(model: MK1-68) three times per week, followed by bioluminescenceimaging one day after each treatment. On day 13 after treatment startmice were sacrificed, perfused with 4% paraformaldehyde, brains wereisolated and fixed overnight in 4% PFA, then transferred to 70% Ethanolfor processing. Mouse brain specimens were serially sectioned andparaffin embedded using standard methods. H&E sections were prepared byroutine methods. Antigen retrieval for immunohistochemistry wasperformed in Tris EDTA pH 8.0 for 30 minutes at 95 degrees Celsius.Slides were treated with blocking reagent (Vector M.O.M. kit BMK-2202)for 32 minutes. Immunohistochemistry was performed using primaryantibodies for Ki67 (Ventana RRF 790-4286, undiluted, room temperaturefor 16 minutes) or cleaved caspase 3 (Cell Signaling #9661, diluted 1:50in M.O.M. diluent, 37 degrees Celsius for 60 minutes). Antibodydetection was performed using the Ventana IView Detection Kit (760-091).

Example 1 Ionizing Radiation Leads to Numerical Chromosomal InstabilityIn Vitro

High-resolution fluorescence microscopy was used to examine varioustypes of errors during anaphase in three human cell lines derived fromnormal human retinal epithelium (RPE1), colorectal cancer (HCT116) orglioma (U251). These cells were either near-diploid and chromosomallystable (RPE and HCT116) or aneuploid and chromosomally unstable (U251).RPE1 and HCT116 had an intact p53-signalling pathway (Thompson et al.Cell Biol. 2010; 188:369-381, whereas U251 contain defective p53signalling (Gomez-Godinez et al. Nucleic Acids Res. 38:e202-e202.(2010). Briefly, cells were exposed to various doses of IR and evaluated25 minutes later for signs of chromosome segregation during anaphase. 25minutes provided sufficient time for many of the cells that were inmitosis during DNA damage induction to enter anaphase, but notsufficient time for cells that were in G2 to proceed through toanaphase. High-resolution fluorescence microscopy revealed that IRexposure leads to a significant increase in anaphase spindles withlagging chromosomes, acentric chromatin fragments, or both (FIGS. 1A and1B). FIG. 1A displays U251 cells fixed 25 minutes following exposure to12 Gy and stained for centromeres using anti-centromere antibody (whitedots), and DNA using (light grey cloud). As demonstrated in FIG. 1A,U251 cells exhibited lagging chromosomes (LC), chromatin bridges (CB),acentric chromatin (AC), or a combination (LC+AC). FIG. 1B showspercentages of chromosome missegregation in response to 0 or 12 Gy IRdose in anaphase spindles of RPE1, U251, and HCT116 cells. The leggingchromosomes evaluated after IR exposure displayed centromere stainingand maintained attachments to microtubules emanating from oppositespindle poles (FIG. 7A). Furthermore, these legging chromosomesexhibited similar levels of staining of γ-H2AX, a marker of DNA doublestand breaks (DSBs), compared with the remaining chromosomes (FIG. 7B).Additionally, the inventors did not observe significant increase inspindles with chromatin bridges (FIGS. 1A-B).

Consequences of IR exposure on chromosome segregation were furtherevaluated by exposure of HCT116 cells to 6 Gy, followed by fluorescencein situ hybridization (FISH) using centromere and telomere probes forchromosome 2 on irradiated nuclei 1 hour later. As shown in FIG. 1C,exposure of non-synchronized cells to IR did not result in significantshort-term change in chromosome number. However, when the cells wereenriched for mitotic cells using a mitotic shake-off method, IR exposureresulted in approximately 2 fold increase in aneuploidy as evidenced bybalanced changes in both centromere and telomere probes specific tohuman chromosome 2 (FIG. 1D).

Example 2 Frequency and Type of Chromosome Segregation Error isDependent on the Time Interval Between Radiation and ChromosomeSegregation Analysis

The inventors sought out to evaluate whether the frequency and types ofchromosome segregation errors are dependent on the time interval betweenIR exposure and the analysis of anaphase chromosome segregation. HCCT116cells devoid of tumor suppressor, p53, were used in this experiment, toallow for the proliferation of aneuploidy cells should they emerge(Thompson and Compton, J Cell Biol. 188(3):369-81, 2010). HCT116 p53−/−cells were exposed to 0 or 6 Gy of IR and chromosome segregation errorswere evaluated at 25 minutes, 12 h, 25 h, and 1 month following the IRexposure. As shown in FIG. 1E, anaphase spindles examined 25 minutesafter irradiation exhibited similar chromosome missegregation profilescompared with p53-competent HCT116 cells 25 minutes after IR exposure.However, 12 h after irradiation there was a significant increase inchromatin bridges and acentric chromatin fragments but not laggingchromosomes (FIG. 1E). Interestingly, anaphase spindles examined 24 h orup to 1 month after IR exposure revealed a significant increase in bothlagging chromosomes and chromatin bridges (FIG. 1E). These findingsindicate that chromosome segregation errors in response to IR exposureare time dependent, where lagging chromosomes peak shortly (25 min)after IR exposure, whereas chromatin bridges peak 12 h later.Importantly, long-term examination (after 1 month) of irradiated cellsshows persistence of lagging chromosomes and chromatin bridges, thehallmarks of w-CIN and s-CIN, respectively.

Example 3 IR Induces w-CIN In Vivo

To determine whether IR can directly perturb the process of chromosomesegregation in vivo, the inventors used tumour-forming HCT116 p53−/−cells that normally exhibit low rates of chromosomes missegregation andare thus considered chromosomally stable and near-diploid (Thompson andCompton, J Cell Biol. 188(3):369-81, 2010). HCT116 p53−/− cells weresubcutaneously injected into nude mice and after 25 days transplantedtumours were exposed to 0 or 10 Gy of IR. Following formalin-fixation oftumours 25 min later, tumour sections were stained with hematoxylin andeosin and the effects of radiation on mitotic cells were evaluated(FIGS. 2A-B). FIG. 2B shows an example of normal anaphase and anaphasecells containing lagging chromosomes in HCT116 p53−/− xenografts afterIR exposure. As demonstrated in FIG. 2C, tumours exposed to 10 Gy of IRexhibited significantly higher rates of chromosome segregation errorsduring anaphase compared with control, non-irradiated, tumours. Intumours from irradiated animals, haematoxylin-stained chromatin wasfrequently visible in the central spindle during anaphase (FIG. 2B andinsets). This chromatin often contained a central constrictionreminiscent of centromeric DNA suggesting that this chromatinencompassed whole chromosomes. However, experimental limitationspreclude us from resolving lagging chromosomes from acentric chromatinfragments with absolute certainty in fixed tumour tissues.

To study the effects of IR on HCT116 p53−/− xenografts in furtherdetail, HCT116 p53−/− xenografts were exposed to varying doses ofradiation (0 Gy, 10 Gy and five daily fractions of 2 Gy over 5consecutive days (FIG. 2D)). As mitotic cells represent a minority ofthe tumour cell population at any given time, the latter fractionatedregimen (2 Gy×5 days) aims at targeting an overall larger number ofmitotic cells over consecutive days. Cells were subsequently derivedfrom irradiated tumours and passaged in culture for an additional 15days to obtain sufficient numbers of cells for karyotype analysis (FIG.2D). Cells derived from non-irradiated tumours displayed mitotic spreadswith near-diploid karyotypes. In contrast, mitotic spreads of cellsderived from irradiated tumours showed significant deviations from thenear-diploid modal chromosome number-particularly those exposed to fivedaily fractions (FIG. 2E). There was also a small increase innear-tetraploid cells, which appeared to have undergone agenome-doubling event (FIG. 2E).

Example 4 Extra-Nuclear DNA Damage in Irradiated Mitotic Cells

In addition to aneuploidy, lagging chromosomes can lead to downstreamdefects that culminate in structural chromosomal damage (Hatch et al.Cell. 154:47-60, 2013), such as the exclusion of lagging chromosomesfrom the primary nucleus in the subsequent G1 phase of the cell cycle,resulting in the formation of micronuclei. RPE1 and U251 cells examined12 h after IR exposure showed increased frequencies ofwhole-chromosome-containing micronuclei that positively stained for bothDNA and centromeres (FIGS. 3A-C).

Next, mitotic U251 cells obtained by mitotic shake-off were irradiatedwith 12 Gy and chromosome spreads examined 24 h after irradiation inorder to assay for chromosome pulverization in the subsequent mitosis aspreviously described by Crasta et al. (Nature. 482:53-58, 2012) (FIG.3D). In these spreads, the appearance of many small chromosome fragmentsand decondensed chromatin indicate the consequences of chromosomepulverization (FIG. 3E). As shown in FIG. 3F, 12 Gy of IR to mitoticU251 cells led to a significant increase in the fraction of chromosomespreads displaying pulverized chromosomes.

To assess the relative levels of DNA damage in the micronuclei comparedwith the primary nuclei, the fluorescence density of γ-H2AX wasevaluated. Without irradiation both primary nuclei and micronuclei hadequivalent densities of γ-H2AX fluorescence, which then significantlyincreased 25 min after IR exposure. As shown in FIGS. 3G and 3H, γ-H2AXdensity in primary nuclei was significantly lower 12 h after IR exposurecompared with 25 min, congruent with DNA repair activity. Conversely,γ-H2AX density in micronuclei was significantly increased at 12 h ascompared with 25 min after IR exposure (FIGS. 3G-H). These findingsindicate that micronuclei are not only defective in DNA repair but canactively generate additional DNA damage. This additional damage islikely the consequence of faulty attempts at DNA repair and defectivemicronuclei nuclear envelope structures. Therefore, by inducing mitoticerrors, IR leads to amplifications of structural chromosomal defectsthat predominantly occur outside of the primary nucleus (extra-nuclear).Unlike DNA damage caused directly by IR, these defects are precipitatedmany hours after IR exposure.

Example 5 Extra-Nuclear Chromosomal Damage Occurs as a Result of MitoticChromosome Segregation Errors

To corroborate the findings from Example 4, which indicate thatextra-nuclear chromosomal damage occurs as a result of mitoticchromosome segregation errors, lagging chromosomes were measured 25 minafter irradiation (0, 2, 6, and 12 Gy) in U251 cells overexpressingGFP-Kif2b (FIG. 3I, FIG. 7C). Kif2b is a microtubule-depolymerizingkinesin-13 protein that specifically corrects erroneous microtubuleattachments to chromosomes (Bakhoum et al. Nat Cell Biol. 2009;11:27-35; Manning et al. Mol Biol Cell. 2007; 18:2970-2979). Itsoverexpression was shown to selectively reduce whole-chromosomesegregation errors and suppression of w-CIN in clonogenic assays in manycancer cell lines, including U251 cells (Bakhoum et al. Nat Cell Biol.2009; 11:27-35). It does so by reducing the stability of microtubuleattachments to chromosomes at kinetochores, which are frequentlyelevated in chromosomally unstable cancer cell lines (Bakhoum et al.Curr Biol. 2009; 19:1937-1942).

As shown in FIG. 3I, U251 cells overexpressing GFP-Kif2b displayedgreater than twofold reduction in chromosome segregation errors duringanaphase compared with control U251 cells, as well as fewer chromosomesegregation errors during anaphase after IR exposure. (FIG. 3I). Insimilar experiments, we found that GFP-Kif2b overexpression reduced thefrequency of IR-induced lagging chromosomes in otherwise chromosomallystable RPE1 cells (Bakhoum Cancer Discov. 2014; 4:1281-1289).Accordingly, GFP-Kif2b overexpression also led to significant reductionsin the frequency of cells containing micronuclei in both RPE1 and U251cells (FIG. 3C). We then examined mitotic spreads, 24 h after exposureof mitotic cells to IR, for downstream chromosomal breaks known toresult from micronuclei.

Next, 24 hours after exposure of mitotic cells to IR, mitotic spreadswere evaluated for downstream chromosomal breaks known to result frommicronuclei. As demonstrated in FIG. 3F, GFP-Kif2b overexpressionsignificantly reduced the incidence of spreads with pulverizedchromosomes. This was not a complete suppression, indicating thatchromosome pulverization in response to IR may also occur throughalternative pathways unrelated to lagging chromosomes.

Example 6 Kif2b Overexpression does not Alter IR-Induced DNA Breaks orRepair

In order to ensure that GFP-Kif2b overexpression does not alter theformation of direct DSBs in irradiated cells or the influence theirability to repair these breaks in primary nuclei, the inventors measuredrelative γ-H2AX fluorescence intensity in irradiated mitotic U251 cells.As shown in FIG. 4A, there was no difference between control andGFP-Kif2b-overexpressing U251 cells. Furthermore, when the averagenumber of γ-H2AX foci in the primary nuclei 20 min after IR exposure wascompared to that of 12 h after IR exposure, there was no significantdifference between control and GFP-Kif2b-overexpressing cells (FIGS.4B-C). As expected, there was an approximately threefold decrease in thenumber of α-H2AX foci 12 h following irradiation in both conditions,owing to DNA DSB repair activity (FIGS. 4B-C). These findings indicatethat suppression of mitotic errors reduces extra-nuclear chromosomaldefects without significantly altering the incidence of DNA DSBs in theprimary nucleus or the rate at which they are repaired.

Example 7 w-CIN Influences Viability of Irradiated Mitotic Cells

Mitosis has long been recognized, for unclear reasons, as the mostradiation sensitive phase of the cell cycle (Terasima et al. Biophys J.1963; 3:11-33; Sinclair et al. Radiat Res. 1966; 29:450-474). Inprevious Examples, the inventors have accomplished to selectively reducechromosome segregation errors without influencing the canonicalIR-induced DNA damage and repair within the primary nucleus. This allowsfor testing whether whole-chromosome segregation errors mightindependently contribute towards the sensitivity of mitotic cells to IR.

Next, the inventors tested the colony-forming ability of U251 cellsover-expressing GFP, GFP-Kif2b, GFP-Kif2a, or GFP-MCAK after exposure ofcells to 0, 2, 4, 6, 8, 10, and 12 Gy. In order to focus on thepotential effects of radiation on cells during mitosis, cells wereenriched for mitotic cells using mitotic shake-off before irradiationand plating for colony growth (FIG. 5A). As shown in FIG. 5A, GFP-Kif2boverexpression led to significant increase in the viability afterirradiation, whereby at 12 Gy of IR, these cells were ˜20-fold moreresistant compared with control cells. Similar to the results observedin U251 cells, GFP-Kif2b overexpression led to increased viability inRPE1 cells as well (FIG. 8A). Importantly, GFP-Kif2b overexpression didnot alter the growth rate of U251 cells in culture or did itsignificantly influence their karyotypic distribution or modalchromosome numbers (FIG. 8B, 8C).

Additionally, overexpression of GFP-MCAK, a second kinesin-13 proteinalso known to suppress w-CIN, led to a similar increase in clonogenicviability of mitotic U251 and RPE1 cells (FIG. 5A and FIG. 7C). On thecontrary, overexpression of either GFP alone or the thirdmicrotubule-depolymerizing kinesin-13 paralogue, GFP-Kif2a, which doesnot reduce chromosome segregation errors during mitosis (Bakhoum et al.Nat. Cell Biol. 11, 27-35 (2009)), did not alter the clonogenicpotential of irradiated cells compared with control (FIGS. 5A and 7C).Interestingly, when U251 cells were irradiated with 0, 2, 4, 6, 8, 10,or 12 Gy as a non-synchronized population that contains only a smallfraction of mitotic cells, overexpression of GFP-Kif2b did not influencethe colony-forming ability (FIG. 5B). Collectively, these resultsindicate that chromosome segregation errors impact the viability ofirradiated mitotic cells as the selective suppression of these errorsthrough destabilization of kinetochore-microtubule stability leads tosignificant increase in mitotic cell resistance to IR.

Example 8 Suppressing w-CIN Leads to Tumour Radiation Resistance

To test the relationship between chromosome segregation errors andtumour response to radiation in vivo, U251 cells expressing fireflyluciferase and either GFP or GFP-Kif2b we intracranially transplantedinto athymic mice. Eighteen days after cell injection, six fractions of4 Gy (24 Gy total) were delivered over a period of 13 days (seeexperimental schema in FIG. 6A). This dose fractionation regimen aimedat targeting the most sensitive subpopulation of tumour cells-whichinclude those undergoing mitosis during IR exposure-over multiple dayswhile allowing cell cycle redistribution in the interval betweenradiation doses. Absolute bioluminescence values before the initiationof treatment increased at comparable rates in GFP- andGFP-Kif2b-overexpressing tumours suggesting similar tumour growth rates(FIG. 9 ). Tumours overexpressing only GFP showed a robust response toradiation treatment as judged by approximately tenfold reduction inluciferase signal at the end of the treatment course (FIGS. 6B-D). Incontrast, there was striking resistance to radiation treatment intumours derived from cells overexpressing GFP-Kif2b (FIGS. 6B-D). Forexample, FIG. 6C shows normalized bioluminescence of intracranial U251xenografts overexpressing GFP or GFP-Kif2b after initiation of IRtreatment. As shown in FIG. 6C, while cells expressing only GFPdisplayed significant response to IR 14 days following the treatment,U251 cells overexpressing GFP-Kif2b exhibited significant resistance toIR at same time points. In order to make sure that the observed resultsare not due to the proliferation differences between the U251 cellsoverexpressing GFP and GFP-Ki2fb, the inventors analyzed the levels ofproliferation marker Ki67. As shown in FIGS. 6E and 6F, overexpressionof Kif2b did not influence cellular proliferation. Moreover, U251xenografts overexpressing GFP or GFP-Kif2b exhibited comparable mitoticindices (FIG. 6G).

GFP- and GFP-Kif2b-expressing tumours also exhibited similar frequenciesof multipolar mitoses known to occur after radiation exposure (Sato etal. Oncogene 19, 5281-5290 (2000)), FIGS. 6H and 6I. However,GFP-Kif2b-expressing tumours displayed decreased apoptosis as indicatedby lower cleaved caspase 3 staining (FIGS. 6J and 6K). Therefore,suppression of numerical chromosomal instability by alteringkinetochore-microtubule attachment stability leads to significantradiation resistance likely by suppressing cell death resultant fromexcessive chromosomal damage.

Example 9 Prophetic Testing Whether Pharmacologically Inducing CINSensitizes TNBC to Radiation Treatment

Maximizing tumor response to radiation treatment represents an importantclinical goal in regionally advanced or metastatic triple negativebreast cancer (TNBC), respectively. In Example 8, the inventors haveshown that suppressing chromosome missegregation rates leads tosignificant tumor radio-resistance in vivo, suggesting that the oppositeact of increasing chromosome missegregation would lead to increase tumorsusceptibility to DNA-damaging therapies.

To test whether increasing CIN sensitizes TNBC to radiation treatment, agenetically engineered mouse model will be used, which recapitulatesgenetic alterations in both BRCA1-related and sporadic TNBC, includingloss of the tumor suppressors p53 and inpp4b with or without brca1(Cancer Genome Atlas Network. Comprehensive molecular portraits of humanbreast tumours. Nature 490, 61-70 (2012)). p53 and brca1 wereconditionally knocked-out through introduction of Cre-recombinase drivenby the Cytokeratin 14 (K14)-promoter and these mice were mated withlittermates heterozygous for inpp4b. Under this genetic background, ˜58%of 60 mice developed spontaneous intraductal carcinomas characterizedwith high-grade pleomorphic nuclei, significant chromosome copy numberalterations (CNAs) and numerous mitoses, highly resembling human TNBC.In addition to this genetically engineered mouse model, patient-derivedxenograft model will be used as well. Briefly, 10⁵ cells will betransplanted in the mammary fat pads of immuno-competent BL6 hosts. Oncetumors reach 5-mm in diameter, 2 Gy daily fractions to a total dose of24 Gy or a biologically equivalent single-dose of 13 Gy will bedelivered using the JLShepherd @ Associates irradiator (model: MK1-68).Animals will then be treated with either placebo or CFI-400945, a smallmolecule inhibitor of Plk4, known to increase chromosome missegregationrates in breast cancer cell lines by inducing supernumerary centrosomesand lagging chromosome formation (Ganem et al. Nature 460, 278-282(2009), Silkworth et al. PLoS ONE 4, e6564 (2009), Mason et al. CancerCell 26, 163-176 (2014)).

Interestingly, breast cancer cell lines are highly dependent on Plk4function and loss of tumor suppressor phosphatase and tensin homolog(PTEN), a frequent occurrence in TNBC, is synthetically lethal with lossof Plk4 activity Brough, R. et al. Cancer Discovery 1, 260-273 (2011)),making the latter an attractive target to further explore in combinationwith established therapies in TNBC.

CFI-400945 will be administered at a concentration of 9.4 mg/kg dailyfor 2 weeks as previously described (Mason et al. Cancer Cell 26,163-176 (2014)). Tumor response will be measured using calipers andbioluminescence imaging. Additionally, measures of the time-to-relapsewill be taken and direct comparison will be made between BRCA-proficientand BRCA-deficient tumors. For statistical methods please see VertebrateAnimals section. Targeted sequencing and FISH will be to used assess thePTEN status of these tumors given the known synthetic lethality with theloss of PTEN and plk4.

Example 10 A Computational Model of CIN in Clonally ExpandingPopulations

Ability to quantitatively study the dynamics of drug resistance andtumor relapse hinges on our capacity to identify, track, and ideallypredict the emergence of resistant tumor subclones. A significantchallenge arises, however, which is to understand the collectivebehavior of tumor cells based on our knowledge of single-cellparameters. To address this and understand how CIN influences theevolution of clonal populations, the inventors developed anexperimentally inspired stochastic model of tumor evolution using theMonte Carlo method and a Markov-chain model (Laughney et al. Cell Rep12, 809-820 (2015)). This model is based on the potency and chromosomaldistribution of oncogenes and tumor suppressor genes on individualchromosomes (Davoli, T. et al. Cell 155, 948-962 (2013)), wherebyclonally expanding population were able to sample the aneuploid fitnesslandscape as they continuously underwent chromosome missegregation.Cellular viability was determined by the chromosomal content such thatmore copies of oncogenic chromosomes led to a higher probability ofcontinued division (FIG. 11A). Tumor viability was then assessed as afunction of chromosome missegregation. Tumor viability was assessed byeither measuring 1) clonal fitness that was defined as the product ofphenotypic heterogeneity and clonal survival or 2) adaptive capacity,which measured how rapidly a clonal population was able to mobilizeacross the aneuploid fitness landscape from a low fitness state to ahigher fitness state. Using these two orthogonal approaches, theinventors found that the viability of tumor cell populations wasmaximized at a chromosome missegregation frequency of 1.9×10⁻³ perchromosome copy per cell division (FIGS. 11B-C). Strikingly, when fourchromosomally unstable cell lines derived from human breast, bone, andcolorectal cancers were experimentally assayed, it was found that theirchromosome missegregation rates fell at or very close to this optimalmissegregation frequency (FIG. 11B). This implies the presence of anevolutionary pressure on chromosome missegregation rates that balanceclonal survival with cellular viability and allows clonal populations torapidly acquire fitter karyotypes. It also provides insight into why CINmay represent a predictive marker of response to therapies that areknown to induce chromosome missegregation (Jamal-Hanjani, M. et al.Annals of Oncology 26, 1340-1346 (2015), Zaki, et al. Cancer 120,1733-1742 (2014)); these therapies likely drive a tumor from an optimalfitness state to a state so chromosomally unstable that it is no longercompatible with viability.

Results by Laughney et al. support the findings disclosed in the presentdisclosure, as they corroborate that cancer cells can tolerate certainlevel of chromosomal segregation errors beyond which they exhibit a“meltdown”. Moreover, the authors provide optimal chromosomemissegregation frequency (1.9×10⁻³) per chromosome copy per celldivision, at which viability of tumor cell populations is maximized.

The present inventors have discovered that increasing chromosomemissegregation together with radiation treatment would lead tosensitization of the tumor to radiation therapy. This in turn permits 1)to decrease dose of radiation and achieve the same effect, 2) tomaintain dose of radiation and increase tumor sensitization in otherwiseresistant tumors, 3) to increase radioprotection of normal organs.

The materials methods and measurements and the particular Examplesdescribed herein are not limiting and the same assessments and practicesof the methods described herein can be made using alternative techniquesknown in the art. All cited references are incorporated by reference intheir entirety.

1.-4. (canceled)
 5. A method for increasing cytotoxicity of ionizingradiation in a subject to be treated for a solid malignant tumorsusceptible to treatment with ionizing radiation comprisingadministering systemically to the subject or locally to the tumor aneffective amount of an enhancer of numerical chromosome instability oran enhancer of chromosome missegregation during mitosis substantiallysimultaneously with or closely preceding or closely following treatmentof the tumor with ionizing radiation.
 6. A method for reducing damage ofnoncancerous cells or tissue incident to ionizing radiation aimed atcancerous cells or tissue comprising exposing the noncancerous cells ortissue to an effective amount of a radioprotective agent which is anenhancer of suppression of chromosome missegregation and reduces numericchromosome instability in said cells simultaneously with or closelyprior to or closely following irradiating the cancerous cells or tissuewith a therapeutically effective dose and regimen of ionizing radiation.7. The method of claim 6 wherein the radioprotection agent is Kif2b,Eg5/Kinesin-5, Polo-like kinase 4, MCAK or NORAD. 8.-9. (canceled)